A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis

Song, Cheng; Zhang, Yingyu; Manzoor, Muhammad Aamir; Wei, Peipei; Yi, Shanyong; Chu, Shanshan; Tong, Zhenzhen; Song, Xiangwen; Xu, Tao; Wang, Fang; Peng, Huasheng; Chen, Cunwu; Han, Bangxing

doi:10.1016/j.ijbiomac.2023.128218

Cited by 3 publications

(3 citation statements)

References 86 publications

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“…Furthermore, BUSCO analysis showed that the annotated genes exhibit 97.3% completeness in the database ( Supplementary Table S6 ). Compared with the newly published P. praeruptorum genome [ 18 ], the data from this study demonstrated high quality in terms of assembly and annotation ( Supplementary Tables S13 and S14 , Supplementary Fig. S10 ).…”

Section: Resultsmentioning

confidence: 89%

“…Several high-quality genomes in Apioideae have been published, including carrot [ 11 ], coriander [ 12 ], celery [ 13 , 14 ], and medicinal plants such as Angelica sinensis [ 15 , 16 ] and Bupleurum chinense [ 17 ]. A chromosomal-level genome of P. praeruptorum was very recently published [ 18 ]. Here, we independently assembled a telomere-to-telomere (T2T) genome of P. praeruptorum along with identifications of genes that coded for enzymes that are involved in the biosynthesis of the medically important coumarins.…”

Section: Introductionmentioning

confidence: 99%

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The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

Bai,

Jiang,

Chu

et al. 2024

GigaScience

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Background Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A–E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies. Results A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins’ spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins. Conclusions A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.

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Section: Resultsmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

Bai,

Jiang,

Chu

et al. 2024

GigaScience

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“…Although the biosynthesis of coumarins has been tentatively demonstrated, the biogenic pathway of furanocoumarins is more challenging to elucidate. Several enzymes that were important for the synthesis of furanocoumarins: prenyltransferase, psoralen synthase and marmesin synthase, did not show any activity when expressed in Escherichia coli (Rodrigues et al, 2022 ; Song et al, 2024 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere

Wang,

Liao,

Pan

et al. 2024

Environ Microbiol Rep

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Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non‐targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP‐binding cassette transporter proteins revealed that some ATP‐binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin.

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Differential involvement of PEBP genes in early flowering of Peucedanum praeruptorum Dunn

Song,

Zhang,

Manzoor

et al. 2024

Postharvest Biology and Technology

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A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis

Cited by 3 publications

References 86 publications

The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere

Differential involvement of PEBP genes in early flowering of Peucedanum praeruptorum Dunn

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